Morphology-based benthic foraminifera indices are increasingly used worldwide for biomonitoring the ecological quality of marine sediments. The recent development of foraminiferal eDNA metabarcoding offers a reliable, time-, and cost-effective alternative to morphology-based foraminiferal biomonitoring. However, the practical applications of these new tools are still highly limited. In the present study, we evaluate the response of benthic foraminifera and define the ecological quality status (EcoQS) in the Bagnoli area (Tyrrhenian Sea, Italy) based on a traditional morphology-based approach and eDNA metabarcoding. The geochemical data show that several sites in front of the former industrial plant contain higher concentrations of potentially toxic elements than the effect range median and are characterized by the highest total organic carbon (TOC) content, whereas the distantly located sites can be considered relatively low- to unpolluted. Significant differences (i.e., diversity and assemblage composition) in both morphological and molecular datasets were found between the relatively low- to unpolluted and the most polluted areas. Similarly, the selected ecological indices of both morphological and molecular datasets strikingly and congruently resulted in a clear separation following the environmental stress gradient. The molecular indices (i.e., g-exp(H'), g-Foram AMBI, and g-Foram AMBI-MOTUs) reliably identified poor-to-bad EcoQS in the polluted area in front of the former industrial plant. On the other hand, the Foram-AMBI based on morphology well identified an overall trend but seemed to overestimate the EcoQS if the traditional class boundaries were considered. The congruent and complementary trends between morphological and metabarcoding data observed in the case of the Bagnoli site further support the application of foraminiferal metabarcoding in routine biomonitoring to assess the environmental impacts of heavily polluted marine areas.
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